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Molina FL, Broquier M, Soorkia S, Grégoire G, Pino GA. Selective Tautomer Production and Cryogenic Ion Spectroscopy of Radical Cations: The Uracil and Thymine Cases. J Phys Chem A 2024. [PMID: 38656804 DOI: 10.1021/acs.jpca.4c02199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The vibrational and electronic spectroscopy of the radical cations of two nucleobases (NB) (uracil and thymine) was studied by cryogenic ion photodissociation spectroscopy. The radical cations have been generated from the photodissociation of NB-Ag+ complexes. A charge transfer process from the NB to Ag+ governs the deactivation mechanism, leading to the formation of the radical cation without further tautomerization. Single- and double-resonance spectroscopy allows for structural assignments of both the silver complexes and the radical cations by comparison with DFT-based calculations. Interestingly, a tautomer-dependent fragmentation is observed in the thymine enol form that involves the loss of NCO, a fragment which was never reported before for this NB. This selective photodissociation of silver complexes containing aromatic chromophore greatly expands the current technique to produce isomer-selected radical cations in the gas phase providing benchmark experimental data to assess calculations of open-shell species.
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Affiliation(s)
- Franco L Molina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- INFIQC: Instituto de Investigaciones en Físico-Química de Córdoba (CONICET-UNC). Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Michel Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Satchin Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Gilles Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
| | - Gustavo A Pino
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- INFIQC: Instituto de Investigaciones en Físico-Química de Córdoba (CONICET-UNC). Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba. Haya de la Torre y Medina Allende. Pabellón Argentina, Ciudad Universitaria, Córdoba X5000HUA, Argentina
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2
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Buczek A, Rzepiela K, Kupka T, Broda MA, Kar T. Uracil-water interaction revisited - in search of single H-bonded secondary minima. Phys Chem Chem Phys 2024; 26:5169-5182. [PMID: 38261334 DOI: 10.1039/d3cp04057g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.
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Affiliation(s)
- Aneta Buczek
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Kacper Rzepiela
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Tapas Kar
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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3
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A DFT study of vibrational spectra of 5-chlorouracil with molecular structure, HOMO-LUMO, MEPs/ESPs and thermodynamic properties. Polym Bull (Berl) 2023; 80:3055-3083. [PMID: 35378874 PMCID: PMC8968244 DOI: 10.1007/s00289-022-04181-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/12/2022] [Accepted: 03/06/2022] [Indexed: 11/04/2022]
Abstract
The density functional theory calculation has been carried out for the analysis of 5-chlorouracil using DFT/Gaussian 09 with GAR2PED. Recorded experimental spectra for Raman and IR of 5-chlorouracil have been analyzed all fundamental vibrational modes using the outcome results of DFT at 6-311++G** of Gaussian 09 calculations and the GaussView 5.09. To help the analysis of vibrational modes, GAR2PED program has been used in the calculation of PEDs. The charge transfer properties of 5-chlorouracil have been analyzed using HOMO and LUMO level energy analysis. HOMO and LUMO energy gap study supports the charge transfer possibility in molecule. These have been made to study for reactivity and stability of heterocyclic molecules for the analysis of antiviral drugs against the new corona virus: COVID-19. Here, the smaller energy gap of 5-chlorouracil is more responsible for charge transfer interaction in the heterocyclic drug molecules and a reason of more bioactivity. The electron density mapping within molecular electrostatic potential plot and electrostatic potential plotting within iso-surface plot have been evaluated the charge distribution concept in the molecule as the nucleophilic reactions and electrophilic sites. These computations have been used to produce the molecular charges, structure and thermodynamic functions of biomolecule. This study has been made to all internal modes of chloro group substituent at pyrimidine ring of C5 atom. The splitting of frequencies has arisen in the two species for the normal distribution modes. Graphical abstract
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4
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Hirao K, Nakajima T, Chan B, Song JW, Bae HS. Core-Level Excitation Energies of Nucleic Acid Bases Expressed as Orbital Energies of the Kohn–Sham Density Functional Theory with Long-Range Corrected Functionals. J Phys Chem A 2020; 124:10482-10494. [DOI: 10.1021/acs.jpca.0c07087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kimihiko Hirao
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
| | - Jong-Won Song
- Department of Chemistry Education, Daegu University, Gyeongsan 113-8656, Korea
| | - Han-Seok Bae
- Department of Chemistry Education, Daegu University, Gyeongsan 113-8656, Korea
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5
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IR and Raman spectra with Gaussian-09 molecular analysis of some other parameters and vibrational spectra of 5-fluoro-uracil. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-020-04101-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Singh J. Thermodynamic functions with other properties and vibrational spectra of pyrimidine ring of uracil for RNA and bio-molecule 5-aminouracil. Heliyon 2019; 5:e02955. [PMID: 31872124 PMCID: PMC6909060 DOI: 10.1016/j.heliyon.2019.e02955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/19/2019] [Accepted: 11/26/2019] [Indexed: 12/03/2022] Open
Abstract
Vibrational spectra (Infra Red and Raman) of uracil and 5-aminouracil have been recorded as well as reproduced in solid phase for the pyrimidinal region (200-2000 cm−1) and the internal modes were analyzed especially for pyrimidine ring of bio-molecules theoretically by using the density functional theory (DFT) calculations on the different basis sets for Restricted Hartree–Fock (RHF) by employing the Gaussian-03 program. These quantum chemical calculations have been employed to yield the Mulliken atomic charges, atomic polarizability tensor (APT) charges and thermodynamic functional properties of these bio-molecules. These DFT calculations have been computed for the some important internal ring modes especially to pyrimidine ring of uracil with a substituent amino-group (NH2) at site of C5 atom on pyrimidine ring.
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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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8
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Castrovilli MC, Bolognesi P, Bodo E, Mattioli G, Cartoni A, Avaldi L. An experimental and theoretical investigation of XPS and NEXAFS of 5-halouracils. Phys Chem Chem Phys 2018; 20:6657-6667. [PMID: 29457179 DOI: 10.1039/c8cp00026c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C, N and O 1s excitation and ionization processes of 5X-uracil (X = F, Cl, Br, and I) were investigated using near edge X-ray absorption fine structure (NEXAFS) and X-ray photoemission (XPS) spectroscopies. This study aims at the fine assessment of the effects of the functionalization of uracil molecules by halogen atoms having different electronegativity and bound to the same molecular site. Two DFT-based approaches, which rely on different paradigms, have been used to simulate the experimental spectra and to assign the corresponding features. The analysis of the screening of the core holes of the different atoms via electronic charge density plots has turned out to be a useful tool to illustrate the competition between the partially aromatic and partially conjugate properties of this class of molecules.
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Affiliation(s)
- M C Castrovilli
- Istituto di Struttura della Materia-CNR, ISM-CNR, Area della Ricerca di Roma 1, CP10, 00015 Monterotondo Scalo, Italy.
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9
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Sohn WY, Kim JJ, Jeon M, Aoki T, Ishiuchi SI, Fujii M, Kang H. Entropic effects make a more tightly folded conformer of a β-amino acid less stable: UV-UV hole burning and IR dip spectroscopy of l-β3-homotryptophan using a laser desorption supersonic jet technique. Phys Chem Chem Phys 2018; 20:19979-19986. [DOI: 10.1039/c8cp02106f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gas-phase spectroscopy of homotryptophan was done to understand conformations of β-peptides.
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Affiliation(s)
- Woon Yong Sohn
- Department of Applied Chemistry
- Faculty of Science and Engineering
- Chuo University
- Tokyo 112-8551
- Japan
| | - Jeong Jin Kim
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
| | - Myeongwon Jeon
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
| | - Takuma Aoki
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Hyuk Kang
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
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11
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Krasnoshchekov SV, Vogt N, Stepanov NF. Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory. J Phys Chem A 2015; 119:6723-37. [DOI: 10.1021/acs.jpca.5b03241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergey V. Krasnoshchekov
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
- Chemieinformationssysteme, Universität Ulm, Albert Einstein Allee 47, D-89069 Ulm, Germany
| | - Natalja Vogt
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
- Chemieinformationssysteme, Universität Ulm, Albert Einstein Allee 47, D-89069 Ulm, Germany
| | - Nikolay F. Stepanov
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
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12
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Singh JS. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:625-640. [PMID: 25244296 DOI: 10.1016/j.saa.2014.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/19/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
FT-IR (400-4000 cm(-1)) and Raman spectra (200-4000 cm(-1)) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G(∗∗) vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a'+13a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 9 modes (5a'+4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3 group are distinctly separated from the CH/NH ring stretching frequencies. Kekule ring stretching mode is found to be comparatively higher frequency magnitude than the mode of uracil due to the involvement of hydrogen bonding of methyl group. But, the ring breathing is found to be lower frequency magnitude compared to those for uracil which could be due to mass effect of the CH3 group in place of the hydrogen atom at the site of C5 atom on pyrimidine ring of uracil.
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Affiliation(s)
- J S Singh
- Department of Physics, Anand Engineering College, Keetham, Agra 282007, India.
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13
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Grimme S, Bauer CA. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:125-140. [PMID: 26307693 DOI: 10.1255/ejms.1313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich- Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany. - bonn.de
| | - Christopher Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany.
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14
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Vogt N, Demaison J, Ksenafontov DN, Rudolph HD. A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of thymine from microwave rotational constants and coupled-cluster computations. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Galvão TLP, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. From 2,4-Dimethoxypyrimidine to 1,3-Dimethyluracil: Isomerization and Hydrogenation Enthalpies and Noncovalent Interactions. J Phys Chem A 2014; 118:4816-23. [DOI: 10.1021/jp503412u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
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16
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Krygowski TM, Szatylowicz H, Stasyuk OA, Dominikowska J, Palusiak M. Aromaticity from the viewpoint of molecular geometry: application to planar systems. Chem Rev 2014; 114:6383-422. [PMID: 24779633 DOI: 10.1021/cr400252h] [Citation(s) in RCA: 366] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tadeusz M Krygowski
- Department of Chemistry, Warsaw University , Pasteura 1, 02-093 Warsaw, Poland
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17
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18
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Stasyuk OA, Szatylowicz H, Krygowski TM. Tautomerisation of thymine acts against the Hückel 4N + 2 rule. The effect of metal ions and H-bond complexations on the electronic structure of thymine. Org Biomol Chem 2014; 12:6476-83. [DOI: 10.1039/c4ob00964a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Not necessarily the π-electron delocalization is responsible for the stability of thymine tautomers.
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Affiliation(s)
- Olga A. Stasyuk
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw, Poland
| | - Halina Szatylowicz
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw, Poland
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19
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Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. Is Uracil Aromatic? The Enthalpies of Hydrogenation in the Gaseous and Crystalline Phases, and in Aqueous Solution, as Tools to Obtain an Answer. J Phys Chem A 2013; 117:5826-36. [DOI: 10.1021/jp404938u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Inês M. Rocha
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
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20
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Khaikin LS, Grikina OE, Vogt N, Stepanov NF. Interpreting the vibrational spectra of uracil molecules and their deuterated isotopomers using a scaled quantum-chemical quadratic force field. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412120102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Szekrényes Z, Kamarás K, Tarczay G, Llanes-Pallás A, Marangoni T, Prato M, Bonifazi D, Björk J, Hanke F, Persson M. Melting of Hydrogen Bonds in Uracil Derivatives Probed by Infrared Spectroscopy and ab Initio Molecular Dynamics. J Phys Chem B 2012; 116:4626-33. [DOI: 10.1021/jp212115h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zsolt Szekrényes
- Institute for Solid State Physics
and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
| | - Katalin Kamarás
- Institute for Solid State Physics
and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
| | - György Tarczay
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös Loránd University, H-1518 Budapest, Hungary
| | - Anna Llanes-Pallás
- Dipartimento di Scienze Farmaceutiche
and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Tomas Marangoni
- Dipartimento di Scienze Farmaceutiche
and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Maurizio Prato
- Dipartimento di Scienze Farmaceutiche
and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Davide Bonifazi
- Dipartimento di Scienze Farmaceutiche
and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
- Department of Chemistry, University of Namur (FUNDP), Rue de Bruxelles 61, 5000
Namur, Belgium
| | - Jonas Björk
- The Surface
Science Research
Centre, The University of Liverpool, Liverpool
L69 3BX, U.K
- Department of Physics,
Chemistry, and
Biology, IFM, Linköping University, 58183 Linköping, Sweden
| | - Felix Hanke
- The Surface
Science Research
Centre, The University of Liverpool, Liverpool
L69 3BX, U.K
| | - Mats Persson
- The Surface
Science Research
Centre, The University of Liverpool, Liverpool
L69 3BX, U.K
- Department of Applied Physics, Chalmers University of Technology, 41296 Göteborg,
Sweden
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22
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Nosenko Y, Kunitski M, Brutschy B. Specific photodynamics in thymine clusters: the role of hydrogen bonding. J Phys Chem A 2011; 115:9429-39. [PMID: 21648386 DOI: 10.1021/jp111373t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.
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Affiliation(s)
- Yevgeniy Nosenko
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-str. 7, 60438 Frankfurt/Main, Germany
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Lee SK, Lee SJ, Ahn AR, Kim YS, Min AR, Choi MY, Miller RE. Infrared Spectroscopy of Imidazole Trimer in Helium Nanodroplets: Free NH Stretch Mode. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.3.885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Shim J, Klobukowski M, Barysz M, Leszczynski J. Calibration and applications of the ΔMP2 method for calculating core electron binding energies. Phys Chem Chem Phys 2011; 13:5703-11. [DOI: 10.1039/c0cp01591a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Giuliano BM, Feyer V, Prince KC, Coreno M, Evangelisti L, Melandri S, Caminati W. Tautomerism in 4-Hydroxypyrimidine, S-Methyl-2-thiouracil, and 2-Thiouracil. J Phys Chem A 2010; 114:12725-30. [DOI: 10.1021/jp106883s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Barbara M. Giuliano
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Vitaliy Feyer
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Kevin C. Prince
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Marcello Coreno
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Luca Evangelisti
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Sonia Melandri
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
| | - Walther Caminati
- Departamento de Química da Universidade de Coimbra, 3004-535 Coimbra, Portugal, Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Dipartimento di Chimica “G. Ciamician” dell’Università, Via Selmi 2, I-40126 Bologna, Italy, and IOM, CNR, Area Science Park, I-34149 Basovizza, Trieste, Italy
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26
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Bravaya KB, Kostko O, Dolgikh S, Landau A, Ahmed M, Krylov AI. Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra. J Phys Chem A 2010; 114:12305-17. [DOI: 10.1021/jp1063726] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oleg Kostko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stanislav Dolgikh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Musahid Ahmed
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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27
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Dautova IF, Ivanov SP, Khursan SL. Hydration effect on the stability of the keto-enol tautomers of 5-hydroxy-6-methyluracil. J STRUCT CHEM+ 2010. [DOI: 10.1007/s10947-009-0162-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Min AR, Lee SJ, Choi MY, Miller RE. Electric Field Dependence Experiments and ab Initio Calculations of Three Cytosine Tautomers in Superfluid Helium Nanodroplets. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.12.3039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Simons J. Good vibrations: probing biomolecular structure and interactions through spectroscopy in the gas phase. Mol Phys 2009. [DOI: 10.1080/00268970903409812] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Chen X, Xing D, Zhang L, Cukier RI, Bu Y. Effect of metal ions on radical type and proton-coupled electron transfer channel: σ-Radical vs π-radical and σ-channel vs π-channel in the imide units. J Comput Chem 2009; 30:2694-705. [DOI: 10.1002/jcc.21284] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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31
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Choi MY, Miller RE. Imidazole dimer and its water complexes formed in superfluid helium nanodroplets: Infrared spectroscopic studies of free OH vibrational stretching modes. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Plekan O, Feyer V, Richter R, Coreno M, Vall-llosera G, Prince KC, Trofimov AB, Zaytseva IL, Moskovskaya TE, Gromov EV, Schirmer J. An Experimental and Theoretical Core-Level Study of Tautomerism in Guanine. J Phys Chem A 2009; 113:9376-85. [DOI: 10.1021/jp903209t] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oksana Plekan
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Vitaliy Feyer
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Robert Richter
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Marcello Coreno
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Gemma Vall-llosera
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Kevin C. Prince
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Alexander B. Trofimov
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Irina L. Zaytseva
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Tatyana E. Moskovskaya
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Evgeniy V. Gromov
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Jochen Schirmer
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
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33
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Lee SJ, Choi MY, Miller RE. Vibrational spectroscopy of xanthine in superfluid helium nanodroplets. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Feyer V, Plekan O, Richter R, Coreno M, Vall-llosera G, Prince KC, Trofimov AB, Zaytseva IL, Moskovskaya TE, Gromov EV, Schirmer J. Tautomerism in Cytosine and Uracil: An Experimental and Theoretical Core Level Spectroscopic Study. J Phys Chem A 2009; 113:5736-42. [DOI: 10.1021/jp900998a] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vitaliy Feyer
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Oksana Plekan
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Robert Richter
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Marcello Coreno
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Gemma Vall-llosera
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Kevin C. Prince
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Alexander B. Trofimov
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Irina L. Zaytseva
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Tatyana E. Moskovskaya
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Evgeniy V. Gromov
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Jochen Schirmer
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti (Rome), I-00016 Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691-Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
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Szyc Ł, Dwyer JR, Nibbering ET, Elsaesser T. Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Kong W, Pei L, Zhang J. Linear dichroism spectroscopy of gas phase biological molecules embedded in superfluid helium droplets. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350802573678] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Gahlmann A, Park ST, Zewail AH. Structure of Isolated Biomolecules by Electron Diffraction−Laser Desorption: Uracil and Guanine. J Am Chem Soc 2008; 131:2806-8. [DOI: 10.1021/ja808720j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Andreas Gahlmann
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, California 91125
| | - Sang Tae Park
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, California 91125
| | - Ahmed H. Zewail
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, California 91125
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Holland D, Potts A, Karlsson L, Zaytseva I, Trofimov A, Schirmer J. A study of the valence shell electronic structure of uracil and the methyluracils. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Krasnokutski SA, Lei Y, Lee JS, Yang DS. Pulsed-field ionization photoelectron and IR-UV resonant photoionization spectroscopy of Al-thymine. J Chem Phys 2008; 129:124309. [DOI: 10.1063/1.2985858] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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40
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Polarization spectroscopy of aluminum phthalocyanine hydroxide embedded in superfluid helium droplets. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Dwyer JR, Szyc L, Nibbering ETJ, Elsaesser T. Ultrafast vibrational dynamics of adenine-thymine base pairs in DNA oligomers. J Phys Chem B 2008; 112:11194-7. [PMID: 18707085 DOI: 10.1021/jp8054119] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-H stretching excitations of DNA oligomers containing 23 alternating adenine-thymine base pairs are studied in femtosecond two-color pump-probe experiments. For a DNA film in a zero relative humidity atmosphere, transient vibrational spectra and their time evolution up to 10 ps demonstrate negligible spectral diffusion and allow for discerning different N-H stretching bands and the O-H stretching absorption of residual water molecules. Lifetimes on the order of 0.5 ps are found for both N-H and O-H stretching modes. The time-dependent pump-probe anisotropies of the different N-H excitations point to a pronounced coupling among them, whereas the O-H stretching anisotropy remains essentially constant.
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Affiliation(s)
- Jason R Dwyer
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
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Vogt N, Khaikin LS, Grikina OE, Rykov AN, Vogt J. Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations. J Phys Chem A 2008; 112:7662-70. [PMID: 18665577 DOI: 10.1021/jp8017138] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.
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Affiliation(s)
- Natalja Vogt
- Chemieinformationssysteme, Universitat Ulm, 89069 Ulm, Germany
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Choi MY, Dong F, Han SW, Miller RE. Nonplanarity of Adenine: Vibrational Transition Moment Angle Studies in Helium Nanodroplets. J Phys Chem A 2008; 112:7185-90. [DOI: 10.1021/jp8012688] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myong Yong Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Feng Dong
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Sang Woo Han
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Roger E. Miller
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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Plekan O, Feyer V, Richter R, Coreno M, de Simone M, Prince K, Trofimov A, Gromov E, Zaytseva I, Schirmer J. A theoretical and experimental study of the near edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of nucleobases: Thymine and adenine. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.021] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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45
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Hu Y, Bernstein ER. Vibrational and photoionization spectroscopy of biomolecules: Aliphatic amino acid structures. J Chem Phys 2008; 128:164311. [DOI: 10.1063/1.2902980] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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46
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Pei L, Zhang J, Kong W. Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets. J Chem Phys 2008; 127:174308. [PMID: 17994819 DOI: 10.1063/1.2803186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to approximately 10% if the permanent dipole is assumed to be approximately 4 debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the pi* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.
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Affiliation(s)
- Linsen Pei
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, USA
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